screen_bam_eff: An efficient function to identify sites of interestes from a...

Description Usage Arguments Value Author(s) Examples

View source: R/screen_bam_eff.R

Description

An efficient function to identify sites of interestes from a list of longitudinal sequence file.

Usage

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screen_bam_eff(file_list, ref = NULL, region, priorPA = 0.001)

Arguments

file_list

A list of bam files.

ref

A referece sequence.

region

An optional region from the BAM file (as a GRanges object)

priorPA

Prior assocation to possible models

Value

PPA association for each site.

Author(s)

Fei Xiang ([email protected])

Examples

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p4305.d3=system.file("extdata/4305-d3.bam",package = "popseq")
p4305.d4=system.file("extdata/4305-d4.bam",package = "popseq")
p4305.d5=system.file("extdata/4305-d5.bam",package = "popseq")
ref=system.file("extdata/A_England_195_2009.fa",package = "popseq")



pigbam=list(p4305.d3,p4305.d4,p4305.d5)


res1=screen_bam_eff(file_list=pigbam,ref=ref,region= GRanges("GQ166656_1",IRanges(1,2280)),priorPA=.001)

res2=screen_bam_eff(file_list=pigbam,ref=ref,region = GRanges("GQ166655_2",IRanges(1,2274)),priorPA=.001)

sdwfrost/popseq documentation built on Aug. 4, 2017, 7:21 p.m.